Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets.
J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity.
Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu
Query: T0542_Ad1.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1j93a_ | Uroporphyrinogen decarboxylase, UROD | UROD/MetE-like | TIM beta/alpha-barrel | α/β |
| Hit | d1m7ja3 | N-acyl-D-aminoacid amidohydrolase, catalytic domain | Metallo-dependent hydrolases | TIM beta/alpha-barrel | α/β |
Query <-- 0.875 --> IntermediateDALI alignment (Z-score: 2.8 Raw score:517.50) query 1 ------------------------------------------------------------ 1 d1j93a_ 1 tqpllldavrgkeverppvwlmrqagrymksyqllcekyplfrdrsenvdlvveislqpw 60 query 1 ------------------------------------------------------------ 1 d1j93a_ 61 kvfrpdgvilfsdiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksvpyv 120 query 1 ------------sLQLRLALN-qidSTVG---------------------------DIAG 20 :::::::: :::: :::: d1j93a_ 121 gealtilrkevnnQAAVLGFVgapfTLASyvveggssknftkikrlafaepkvlhaLLQK 180 query 21 NAEAILRWTRHSAEQGAHLVAFPEMaltgypvedLALRSSFVEASRTALRELAARLAEEg 80 ::::::::::::::::::::::::: ::::::::::::::::::::::::: d1j93a_ 181 FATSMAKYIRYQADSGAQAVQIFDS------watELSPVDFEEFSLPYLKQIVDSVKLT- 233 query 81 FGELPVLVGY---lDRSEsaqpkygqpagaprnaaavlhrgRVALTFAKHhlpnygvfde 137 :::::::::: :::: ::::::::: d1j93a_ 234 HPNLPLILYAsgsgGLLE------------------rlpltGVDVVSLDW---------- 265 query 138 fryfvPGDTMpivrlhgvdialaiceDLWQD----ggrvPAARSAGaglllsvnaspyer 193 ::::: ::::: ::::::: d1j93a_ 266 -----TVDMAdgrrrlgpnvaiqgnvDPGVLfgskefitNRINDTV---kkagkgkhiln 317 query 194 dkddtRLELvRKRAQEAGcttaylamiggqdelvfdgdsivvdrdgevvarapqfsegcv 253 :::: :::::::: d1j93a_ 318 lghgiKVGTpEENFAHFF------------------------------------------ 335 query 254 vldldlpaaEAEPptgvvddglridrlviseeplpayeaelaggyadrl 302 :::: d1j93a_ 336 -----eiakGLRY------------------------------------ 343 FAST alignment (Normalized score: 2.91 Raw score:937.50) query 1 S----------------------------------------------------------- 1 d1j93a_ 1 -TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQP 59 query 2 ------------------------------------------------------------ 2 d1j93a_ 60 WKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY 119 query 2 --------------LQLRLALNQIDSTV-------------------------------- 15 :::::::: d1j93a_ 120 VGEALTILRKEVNNQAAVLGFV------GAPFTLASYVVEGGSSKNFTKIKRLAFAEPKV 173 query 16 --GDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLAL--------RSSFV-EA 64 ::::::::::::::::::::::::::: ::::: :: d1j93a_ 174 LHALLQKFATSMAKYIRYQADSGAQAVQI---------------FDSWATELSPVDFEEF 218 query 65 SRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRG------ 118 :::::::::::::: :::::::::: d1j93a_ 219 SLPYLKQIVDSVKL-THPNLPLILY-----------------------------ASGSGG 248 query 119 --------RVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVD-------------- 156 ::::::: d1j93a_ 249 LLERLPLTGVDVVSL-------------------------------DWTVDMADGRRRLG 277 query 157 ---IALAICEDLWQDG------------------GRVPAARSAGA---GLLLSV---NAS 189 ::::: ::::: ::::: ::: d1j93a_ 278 PNVAIQGN--------VDPGVLFGSKEFITNRINDTVKK------AGKGKHIL-NLGHGI 322 query 190 PYERDKD-----DTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVAR 244 : ::::::::::: d1j93a_ 323 K------VGTPEENFAHFFEIAK------------------------------------- 339 query 245 APQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRL-- 302 d1j93a_ 340 ----------------------------------------------------------GL 341 query 303 -- 303 d1j93a_ 342 RY 343 TMalign alignment (TM-score: 0.44 Raw score:131.70) query 1 SLQLRL------------------------------------------------------ 6 ::::: d1j93a_ 1 -TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQP 59 query 7 ------ALNQIDSTVGDIAGN--------------------------------A---E-A 24 ::::::::::::::: : : : d1j93a_ 60 WKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY 119 query 25 ILRWTRHSAE--QGAHLVAFPEMAL-TG-YP-----VE--D-LAL---------RSSFVE 63 :::::::::: ::::::::::::: :: :: :: : ::: :::::: d1j93a_ 120 VGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQ 179 query 64 ASRTALRELAARLAEEGFGELPVLVGYLDRS--ESAQPKYGQPAGAPR-NAA-AV--LHR 117 :::::::::::::::: : ::::::::::: : :::::::::: ::: :: ::: d1j93a_ 180 KFATSMAKYIRYQADS-G--AQAVQIFDSWATE---L-SPVDFEEFSLPYLKQIVDSVKL 232 query 118 GRV-ALTFA-KHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAA 175 ::: ::::: :::::: : :::::::::: ::::::::::::::::: d1j93a_ 233 THPNLPLILYASGSGG------L--LERLPLTGVD--------VVSLDWTVDMADGRRRL 276 query 176 RSAGAGLLLSVNASPYERDKDD--TRLELVRKRAQEAGCT-TAYLA-MIGGQDELVFD-G 230 ::: : ::::::: ::::::: :::::::::::::::: ::::: ::: :::: : d1j93a_ 277 GPN-V--AIQGNVD-PGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGI----KVGTPE 328 query 231 --DSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLP 288 ::::: ::::: ::: d1j93a_ 329 ENFAHFF---EIAKG-------------LRY----------------------------- 343 query 289 AYEAELAGGYADRL 302 d1j93a_ 344 -------------- 344 HHsearch alignment (Probability: 0.14 E-value:0.02) query 18 IAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSSFVEASRTALRELAARLA 77 ::::::::::::::::::::::::::::::::::::: ::::::::::::::::: d1j93a_ 178 LQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVD------FEEFSLPYLKQIVDSVK 231 query 78 EEGFGELPVLV 88 :::: :::::: d1j93a_ 232 LTHP-NLPLIL 241
Intermediate <-- 0.739 --> HitDALI alignment (Z-score: 7.5 Raw score:925.60) d1j93a_ 1 tqpllldavrgkeverpPVWLMRQagrymksyqllcekyplfrdrsenvdlvveiSLQP- 59 ::::::: :::: d1m7ja3 1 ---------------gfIDSHTHD-------------------------------DNYLl 14 d1j93a_ 60 ---wKVFR------PDGVI----LFSDiltplsgmnipfdiikGKGPvifdplrtaadve 106 :::: ::::: :::: :::: d1m7ja3 15 khrdMTPKisqgvtTVVTGncgiSLAP-------------lahANPP----------apl 51 d1j93a_ 107 kvrefipeksVPYVGEALTIL-rkevnnQAAVLGFVG--apftLASYVVeggssknftki 163 ::::::::::: ::::::::: :::::: d1m7ja3 52 dlldeggsfrFARFSDYLEALraappavNAACMVGHStlraavMPDLRR----------- 100 d1j93a_ 164 krlafaepkvlhaLLQKFATSMAKYIRYQADSGAQAVQIFDSWatelspvdfeeFSLPYL 223 :::::::::::::::::::::::::::::: :::::: d1m7ja3 101 ------------eATADEIQAMQALADDALASGAIGISTGAFY------ppaahASTEEI 142 d1j93a_ 224 KQIVdSVKLTHpNLPLILYASG----SGGLLERLPLTG-----vDVVS-LDWT-----vD 268 :::: :::::: :::::::::: :::::::::::: :::: :::: : d1m7ja3 143 IEVC-RPLITH-GGVYATHMRDegehIVQALEETFRIGreldvpVVIShHKVMgklnfgR 200 d1j93a_ 269 MADGRRRLGP-----NVAIQGnvdPGVL-------------------------------- 291 :::::::::: :::::: :::: d1m7ja3 201 SKETLALIEAamasqDVSLDA-ypYVAGstmlkqdrvllagrtlitwckpypelsgrdle 259 d1j93a_ 292 ---------------------fgskefitNRINDTVKKagkGKHILN-lghgiKVGTPEe 329 ::::::::: :::::: :::::: d1m7ja3 260 eiaaergkskydvvpelqpagaiyfmmdePDVQRILAF---GPTMIGsdglphDERPHP- 315 d1j93a_ 330 NFAHFFEIAK-GLRY---------------------------- 343 :::::::::: :::: d1m7ja3 316 RLWGTFPRVLgHYSRdlglfpletavwkmtgltaakfglaerg 358 FAST alignment (Normalized score: 3.13 Raw score:1099.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 d1m7ja3 1 ------------------------------------------------------------ 1 d1j93a_ 61 KVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVP-- 118 d1m7ja3 1 ----------------------------------------------------------GF 2 d1j93a_ 119 ------------------------------------------------------------ 119 d1m7ja3 3 IDSHTHDDNYLLKHRDMTPKISQGVTTVVTGNCGISLAPLAHANPPAPLDLLDEGGSFRF 62 d1j93a_ 119 -YVGEALTILRKEVNN-----QAAVLGFVGA---PFTLASYVVEGGSSKNFTKIKRLAFA 169 ::::::::::: ::::::: :::: d1m7ja3 63 ARFSDYLEALRA----APPAVNAACMVG---HSTLRAA---------------------- 93 d1j93a_ 170 EPKVLHAL---------LQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEF-- 218 ::::::::::::::::::::::::::: d1m7ja3 94 --------VMPDLRREATADEIQAMQALADDALASGAIGISTGA--------------FY 131 d1j93a_ 219 ------SLPYLKQIVDSVKLTHPNLPLILYAS-------GSGGLLERLPLTGVDVVSLDW 265 :::::::::::::: ::::::: ::::::::::: d1m7ja3 132 PPAAHASTEEIIEVCRPLIT--HGGVYAT---HMRDEGEHIVQALEETFR---------- 176 d1j93a_ 266 TV-----------------------DMADGRRRLG-------PNVAIQGNVDPGVLFGSK 295 :::::::: ::::: d1m7ja3 177 --IGRELDVPVVISHHKVMGKLNFGRSKETLAL--IEAAMASQDVSL------------- 219 d1j93a_ 296 EF---------------------------------------------------------- 297 d1m7ja3 220 --DAYPYVAGSTMLKQDRVLLAGRTLITWCKPYPELSGRDLEEIAAERGKSKYDVVPELQ 277 d1j93a_ 298 ---------ITNRINDTVKKAG-KGKHILNLGHGIKVGTPEENF----------AHFFEI 337 ::::::::: ::::::: :::::: d1m7ja3 278 PAGAIYFMMDEPDVQRIL----AFGPTMIG--------------SDGLPHDERPHPRLWG 319 d1j93a_ 338 AKGLRY------------------------------------ 343 ::: d1m7ja3 320 TFP---RVLGHYSRDLGLFPLETAVWKMTGLTAAKFGLAERG 358 TMalign alignment (TM-score: 0.49 Raw score:167.36) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSY---------------------QLLC-EK 38 ::::::::::::::::: :: : d1m7ja3 1 ---------------GFIDSHTHDDNYLLKHRDMTPKISQGVTTVVTGNCGIS--LAP-L 42 d1j93a_ 39 YPL-F-----------RDRSENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFD 86 ::: : ::::::::::::::::::::::: ::::::::::::: ::: d1m7ja3 43 AHANPPAPLDLLDEGGSFRFARFSDYLEALRAAPPAVNA--ACMVGHSTLRAAV--MPD- 97 d1j93a_ 87 IIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFT 146 : :: : :::::::::::::::::::: ::::::: :: d1m7ja3 98 --------L--RR-----E--ATADEIQAMQALADDALASG---------AIGISTG-AF 130 d1j93a_ 147 LASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSW 206 : :::: : :::::::::::::::::: :::::: : d1m7ja3 131 Y-PPAA------------------------H--ASTEEIIEVCRPLITHGG-VYATHM-R 161 d1j93a_ 207 ATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSG----G-LL-ERLPLT--G- 257 :: :: :::: :::::::::::: : ::::::::::: : :: :::::: : d1m7ja3 162 DE-GE--HIVQ-ALEETFRIGREL---D--VPVVISHHKVMGKLNFGRSKETLALIEAAM 212 d1j93a_ 258 ---VDVVSLDWTV----------------------------------------------- 267 :::::::::: d1m7ja3 213 ASQDVSLDAYPYVAGSTMLKQDRVLLAGRTLITWCKPYPELSGRDLEEIAAERGKSKYDV 272 d1j93a_ 268 ---------------D--MADGRRRLGPNVAIQGNVDP--------GVLFGSKEFITNRI 302 : :::::: : : :::::::: ::::: ::::: d1m7ja3 273 VPELQPAGAIYFMMDEPDVQRILA-F-G--PTMIGSDGLPHDERPHPRLWG----TFPRV 324 d1j93a_ 303 ND-TVK----KA--GKGKHILN----------LGHGIKVGTPEENFAHFFEIAKGLRY 343 :: ::: :: :::::::: : : d1m7ja3 325 LGHYSRDLGLFPLETAVWKMTGLTAAKFGLAE---------------------R-G-- 358 HHsearch alignment (Probability: 0.01 E-value:0.47) d1j93a_ 221 PYLKQIVDSVKLTH 234 :::::::::::::: d1m7ja3 169 QALEETFRIGRELD 182